February 17, 2015
## brain ## 2m_APP 2m_WT 4m_APP 4m_WT 5m_APP 5m_WT 6m_APP 6m_WT ## 5 5 9 13 18 13 8 11
## retina ## 2m_APP 2m_WT 5m_APP 5m_WT 6m_APP 6m_WT ## 4 5 3 5 5 6
\(y \sim age + group + batch + age * group\)
load(file = "markdown/fit_app.rdt") fit.app$coefficients
## Estimate Std. Error t value Pr(>|t|) ## (Intercept) 10.49802829 0.01860672 564.2062503 8.932371e-97 ## age4m -0.01065783 0.02362574 -0.4511110 6.538600e-01 ## age5m -0.03710797 0.02189447 -1.6948560 9.632304e-02 ## age6m -0.06244793 0.02436192 -2.5633422 1.342184e-02 ## groupAPP 0.96882037 0.02749563 35.2354293 5.690012e-37 ## batchmouse -0.04023277 0.01993577 -2.0181194 4.896016e-02 ## age4m:groupAPP 0.04023281 0.03526372 1.1409121 2.593418e-01 ## age5m:groupAPP 0.05077686 0.03259252 1.5579297 1.255577e-01 ## age6m:groupAPP 0.02422343 0.03673571 0.6593974 5.126664e-01
## groupAPP age4m:groupAPP age5m:groupAPP age6m:groupAPP ## Zfp930 FALSE FALSE FALSE FALSE ## Zfp941 TRUE FALSE TRUE TRUE ## Znhit1 FALSE FALSE FALSE FALSE
## age4m age5m age6m age4m:groupAPP age5m:groupAPP age6m:groupAPP ## Zfp930 FALSE FALSE FALSE FALSE FALSE FALSE ## Zfp941 FALSE FALSE TRUE FALSE TRUE TRUE ## Znhit1 FALSE FALSE FALSE FALSE FALSE FALSE
profile.Id
## [1] "FALSE-TRUE-TRUE-FALSE" "TRUE-FALSE-FALSE-TRUE" ## [3] "TRUE-TRUE-FALSE-FALSE" "FALSE-FALSE-TRUE-TRUE" ## [5] "FALSE-TRUE-FALSE-TRUE" "TRUE-FALSE-TRUE-FALSE" ## [7] "FALSE-FALSE-TRUE-FALSE" "TRUE-FALSE-TRUE-TRUE" ## [9] "TRUE-FALSE-FALSE-FALSE" "FALSE-FALSE-FALSE-TRUE"
Gene number: 61
## KEGGID Pvalue Term ## 1 05010 0.0002631084 Alzheimer's disease ## 2 03010 0.0028387608 Ribosome ## 3 00190 0.0054019260 Oxidative phosphorylation ## 4 04744 0.0095038471 Phototransduction
Gene number: 173
## KEGGID Pvalue Term ## 1 03010 1.311303e-08 Ribosome ## 2 04020 1.394302e-03 Calcium signaling pathway ## 3 00330 4.113916e-03 Arginine and proline metabolism ## 4 05322 9.474179e-03 Systemic lupus erythematosus ## 5 04720 9.798741e-03 Long-term potentiation
Gene number: 179
The 278 genes that separate the 2 groups
The 278 genes that separate the 2 groups
61 GLM APP genes
133 GWAS AD genes and 61 GLM APP genes
## Estimate Std. Error t value Pr(>|t|) ## (Intercept) 5.431993400 0.02902422 187.15384094 7.932439e-73 ## age4m 0.050087235 0.03685327 1.35909889 1.802143e-01 ## age5m -0.017508569 0.03415270 -0.51265546 6.104498e-01 ## age6m -0.072281386 0.03800162 -1.90206074 6.293165e-02 ## groupAPP 0.005948535 0.04288983 0.13869336 8.902496e-01 ## batchmouse -0.058435065 0.03109737 -1.87909967 6.606587e-02 ## age4m:groupAPP -0.002872924 0.05500710 -0.05222823 9.585549e-01 ## age5m:groupAPP 0.006968397 0.05084036 0.13706428 8.915304e-01 ## age6m:groupAPP 0.137731629 0.05730323 2.40355769 1.998603e-02
## branch ## 0 1 2 3 4 5 6 7 8 ## 99 191 159 100 69 61 58 56 49
## [1] "2900079G21Rik" "Abhd14b" "Acat2" "Aldh1a2" ## [5] "App" "Arpp21" "Arrdc1" "BC051226" ## [9] "Cd97" "Chordc1" "Creld2" "Cryab" ## [13] "Cys1" "Dhcr24" "Dnajb11" "Dnajc3" ## [17] "E130307A14Rik" "Fdft1" "Fdps" "Gm6741" ## [21] "Gm7120" "Gstk1" "Hsp90b1" "Hspa1b" ## [25] "Hspa5" "Hspb1" "Insig1" "Iqgap2" ## [29] "Klhl29" "Lamr1-ps1" "Lime1" "Magt1" ## [33] "Manf" "Mapk12" "Mas1" "Mical1" ## [37] "Mllt3" "Nsdhl" "Pdia3" "Pdia4" ## [41] "Pdia6" "Prnp" "Psen1" "Pstpip2" ## [45] "Rab34" "Rps6ka5" "Sars2" "Sc4mol" ## [49] "Sdf2l1" "Sh3rf3" "Simc1" "Slc6a13" ## [53] "Spice1" "Srebf1" "Stard4" "Stx2" ## [57] "Taf6l" "Tnni1" "Tox" "Wdr6" ## [61] "Xbp1" "Zdhhc14" "Zfp316"
## [1] "Mllt3" "Srebf1" "Taf6l" "Xbp1"
63 Module 6 genes
133 GWAS AD genes and 63 Module 6 genes
## Estimate Std. Error t value Pr(>|t|) ## (Intercept) 4.55777975 0.04624779 98.5512945 6.119811e-59 ## age4m -0.04252858 0.05872277 -0.7242265 4.723020e-01 ## age5m -0.10883739 0.05441963 -1.9999658 5.095089e-02 ## age6m -0.09890929 0.06055257 -1.6334448 1.086576e-01 ## groupAPP -0.14849526 0.06834155 -2.1728400 3.455778e-02 ## batchmouse 0.08846152 0.04955121 1.7852547 8.028640e-02 ## age4m:groupAPP 0.05468232 0.08764947 0.6238751 5.355457e-01 ## age5m:groupAPP 0.10056666 0.08101009 1.2414090 2.202471e-01 ## age6m:groupAPP 0.10582645 0.09130817 1.1590031 2.519604e-01